Managing editor Lionel Morais, features editor Zulkifli Sulong and Malay news editor Amin Iskandar were taken into custody and several computers and other items were confiscated.
Authorities in socially conservative Malaysia have conducted a series of arrests since last August for sedition, detaining opposition politicians, activists, and academics. Nurul Izzah Anwar, the daughter of jailed opposition leader Anwar Ibrahim, was arrested for sedition this month over a speech made in parliament.
The latest arrests were over an article that said the Confederation of Rulers - Malaysia's monarchy - had rejected a proposal to amend a federal law that could allow the use of the Islamic punishment, hudud, in Malaysia.
Malaysia's Islamist opposition party is calling for strict enforcement of sharia, or Islamic law, for Muslims that includes amputations and stonings.
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"This started out as the cops wanting to question the editors and take statements," said Syahredzan Johan, a lawyer representing the company. "We only knew they wanted to make arrests after they came to the office".
Police and officials from the MCMC are investigating Morais, Sulong and Iskandar for sedition and improper use of network service that is "obscene, indecent, false, menacing or offensive in character", Johan said.
Police also confirmed the three men had been detained and were under investigation.
Malaysia's Sedition Act, which dates from British colonial times, criminalizes speech with an undefined "seditious tendency". Critics have said the government has used the law to silence dissent, preventing open debate and discussion.
The government says the law is necessary to clamp down on inflammatory actions that could stir ethnic or religious tension. Prime Minister Najib Razak, who had pledged to repeal the act in 2012, bolstered it last year to protect the sanctity of Islam and the Malaysia's traditional rulers, the sultans.
The previous arrest for sedition involving a media worker was in September 2014, when a reporter from news portal Malaysia Kini was taken in for questioning but later released.